ABOUT
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This zip file contains all the files you need in order to run the protocol "Rosetta and the design of ligand binding site".
First unzip the file, the main program running is 'runRosetta'. For more details run:
	./runRosetta.sh -h

BEFORE YOU START
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You need to download:
	* ligand file in MOL2 format
		a good place to start looking is 'http://zinc.docking.org'
	* ligand binding protein (receptor) in PDB format
Make sure you installed:
	* Rosetta software
	* BCL
	* Open Bable
	* Python
	* Chimera or any other visualisation software (optional)
After you got all softwares installed, edit 'runRosetta' file to include the path to the softwares. 
(insert path under 'deifne variables' section)
	
STEPS
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The main program 'runRosetta' is used to run all the steps in the protocol.
STEP 1: pre-relax the protein. to run this step:
	./runRosetta -s 1 -r <receptor file name WITHOUT extension>

STEP 2: prepare the ligand. to run this step:
	./runRosetta -s 2 -l <ligand file name WITHOUT extension>
	Troubleshooting:
	- maybe you need to edit 'runRosetta' and remove the line with 'source ${BCL}/setup.sh' (system depended)
	- academic license of BCL can be for just one week. try to update the license and then run again.

STEP 3: place the ligand into the protein
	this step done manully. see the attached pdf file 'Step3.3-Place_the_ligand_into_the_protein.pdf'

STEP 4: run rosetta design. to run this step:
	./runRosetta -s 4 -l <ligand file name WITHOUT extension> -r <receptor file name WITHOUT extension> -m <number of output models>
	This is the longest step that require strong computing power.

STEP 5: filter designs. to run this step:
	./runRosetta -s 5 
	The results are being filtered according to the filters in the CONFIG files.
	If you want to remove or add filters just edit the '<results/interfaces>_metrics.config' file.
	To reset the config files run the python script 'write_config.py'
	*ATTENTION:* some of the filters are static (don't have a dynamic threshold). 
	   Therefor they are hard coded in the 'calc_metric_thresholds.py' or 'calc_metric_thresholds2.py' in the end of the file.
	   ('calc_metric_thresholds.py' is for results filtering and 'calc_metric_thresholds2.py' is for interface filtering)
	Filtered disgnes can be found in the 'filtered_pdbs.txt' file.
	
STEP 6: run new cycle. this step is not part of the protocol. to run this step:
	./runRosetta -s 6 -l <ligand file name WITHOUT extension> -r <receptor file name WITHOUT extension> -m <number of output models>
	This step is very similar to step 4, but running against all the designs in 'filtered_pdbs.txt'.
	Try to decrease the number of output models in this step, even by half.
	You should run step 5 again to filter the new results. 
	
SUMMARY
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Enjoy your Rosetta designing!
In any problem you can contact us: technionigem2016@gmail.com
Technion iGEM 2016